Thursday, September 15, 2011

The Amyloid Threat, Big Numbers Game and Quote Mining: Protein Evolution and How Evolutionists Respond to the Empirical Evidence

Even by the evolutionist’s own numbers protein evolution has failed by somewhere between 27 to 49 orders of magnitude. And those estimates—which make evolution unquestionably the worst theory in science—are optimistic. They are based not on the evolution of a protein, but only part of a protein. But even worse, those estimates assume, believe it or not, the prior existence of proteins. That’s right, when evolutionists estimated the number of searches evolution could have made for those elusive protein sequences, they assumed billions of bacteria were available to do the job. But to synthesize a protein, bacteria need hundreds of different types of, yes, proteins. Indeed, to be bacteria, they need an army of proteins. So we cannot sneak in billions of bacteria when trying to show that evolution can create proteins. If we are going to argue that X could have evolved, we are not allowed to assume the prior existence of X. Nonetheless the evolutionists did just that, and concluded:

We hope that our calculation will also rule out any possible use of this big numbers ‘game’ to provide justification for postulating divine intervention.

As usual divine intervention is the target and ruling it out is the motivation for the pseudo science. For evolution’s theoretical core, as Lakatos would put it, is not gradualism or selection, but naturalism.

Gradualism and selection are two of the many explanations of how evolution occurred, a topic that is always up for grabs because evolution is so unlikely. But despite its many scientific problems, evolutionists insist that evolution must have occurred. It is a fact, no question about it. Divine intervention is strictly disallowed, for otherwise we would be faced with all those unthinkables. The problem is not with the “divine,” it is with the “intervention.” That’s a no-no. So much for the separation of church and state.

Another problem: Protein aggregation

But science knows none of this. It continues on its inexporable march toward truth. One finding long hypothesized, that further aggravates the problem of protein evolution, is that what seem to be perfectly good proteins, in fact, have a propensity to stick to each other and form fibrils. Like a crystal, multiple copies of a protein can attach and form a growing and dangerous amyloid fibril.

The cell’s solution to this that the sticky patches on proteins, which cause the proteins to aggregate, are conveniently tucked away in the protein’s interior when it folds up. Furthermore, the cell is equipped with a variety of mechanisms to guard against aggregation, and detect and destroy fibrils when they do occur.

All of this simply creates more problems for the evolution narrative. Not only are proteins unlikely to evolve, but even if evolution somehow performs miracle after miracle, it must also ensure those sticky patches are not exposed, and evolution will rapidly need those additional safeguard mechanisms, with the hundreds of, yes, proteins they require.Reader comments

But evolutionists will have none of this. As usual they are unfazed by empirical evidence. One evolutionist in the know commented:

Cornelius Hunter, 2011, paraphrased (blogpost): "It is too easy for proteins to evolve to bind to each other. Therefore, evolution is impossible."

Michael Behe, 2007, paraphrased (Edge of Evolution): "It is too hard for proteins to evolve to bind to each other. Therefore, evolution is impossible."

That’s funny, and perhaps more tongue-in-cheek than serious, but to be clear the amyloid state is caused by the binding of short, self-complementary protein sequences which have a relatively high propensity to stick to themselves. These self-complementary sequences are fairly common. The quaternary binding surfaces to which Behe refers, on the other hand, are far more elusive and difficult to generate at random.

The kinds of numbers games that Dr Hunter likes to play may be amusing to some, but they are futile at our current state of ignorance. … To disparage evolution for not being able to offer an explanation for every event in the history of life is a cheap shot, much favored by creationists.

Evolutionists insist that science completely and unequivocally confirms evolution, but when the evidence is presented to them they appeal to our ignorance and future resolution of the problems.

Of course no one knows what the future findings will reveal. That is the nature of science. But when we claim a theory is a fact, we are referring to our current knowledge. Evolutionists cannot claim their idea is a fact, beyond a shadow of a doubt, while simultaneously denying the empirical evidence. The evolutionist later continued:

The frivolity is in his probability calculations. Such calculations depend on such questionable assumptions that they are scientifically useless - though they seem to be useful to anti-evolution apologists.

Actually, while the evolutionist’s assumptions are “questionable,” as discussed above, even these estimates from the evolutionists themselves show how severely the evidence contradicts evolution. The evolutionary shortfall is between 27 orders of magnitude and 49 orders of magnitude, according to the evolutionist’s own numbers. So these probabilities do not come from me, they come from evolutionists. In fact, this same evolutionist had once recommended the paper which he now disparages. So what an evolutionist writes is good science. But when repeated by a skeptic, it becomes a frivolous “numbers game.”

Another evolutionist denied that contrary evidence is important:

Saying that something is unlikely really doesn't mean anything on it's own. A hypothesis can be extremely unlikely and still be correct. This is a point that Cornelius simply refuses to understand.

Actually I agree with this point. My point is not that evolution is false, as this evolutionist seems to think. The problem is not so much with the idea of evolution, which is empirically unlikely, but with the evolutionist’s insistence that it is a fact.

As I have explained many times, this “fact” claim is an epistemological claim. It is a claim about the state of our knowledge. I do not know whether evolution occurred or not. But I do know that it is not a fact. The protein evolution evidence discussed above is one example of why it is not a fact. So contrary to this evolutionist’s claim, saying that something (such as evolution) is unlikely really does mean something. It means it is not a fact.

Another evolutionist said that I was ignoring an obvious solution to the problem:

[T]hat's why so many of us have problems with CH's lack of honesty. The paper CH continually cites shows nothing of the sort. It says the protein couldn't evolve in that time frame by adaptive walking only. But then the paper goes on to add that adaptive walking isn't the only mechanism at work, that there are other known mechanisms such as homologous recombination that greatly shorten the timeline. So there's no huge time problem.

CH loves to quote-mine the first part of the summary but always forgets to include the later explanation.

Here is the quote this evolutionist refers to:

Such a huge search is impractical and implies that evolution of the wild-type phage must have involved not only random substitutions but also other mechanisms, such as homologous recombination.

I have discussed this several times, such as here and here. Homologous recombination is a complex genetic mechanism assisted by, yes, finely-tuned proteins. As with the bacteria example above, it is circular to recruit such a mechanism for the initial evolution of proteins—for no such mechanism is likely to have existed.

And even if homologous recombination could somehow have been in play, it wouldn’t help anyway. For while this is a clever mechanism for the swapping of nature’s protein modules, it does not help when used with sequences that are nowhere close to solving the problem. Jumping from one local peak in sequence space to another doesn’t improve the odds in finding the astronomical, one-in-10^70, longshot.

Finally, an evolutionist attacked a common strawman:

The "amyloid threat" that you mention poses a challenge to science only if you assume that the functional state of a protein must be its most thermodynamically stable state. But this is not a valid assumption since evolution does not aim for the all-time best possible protein structure in terms of stability but one that is stable enough to perform the intended function.

It is true that the “amyloid threat,” as he puts it, poses no threat to science. I never made such a claim. It does pose yet another problem, however, for evolution. And none of this assumes that the functional state of a protein must be its most thermodynamically stable state. Indeed, it may not be for many proteins, but that is a separate issue. He continued:

The error in your thinking is a common one, that of assuming that evolution must somehow aim toward an ideal situation (in this case thermodynamically most stable structure). The reality is that evolution can only work on what already exists, which often is far from being the best possible set of solutions.

Except that I made no such assumption.

Evolution, even with extremely optimistic assumptions, is easily the worst scientific theory. One can find theories that may be unlikely, but evolution’s shortfall, of 27 orders of magnitude (and that is assuming a biosphere teeming with life already exists), is extreme.

That does not mean future findings won’t somehow reverse our current knowledge. Nor does it mean that our current knowledge falsifies evolution. Though most scientists would drop a theory with such astronomically unlikely probabilities, low probability—even incredibly low probability—cannot insure that an idea is false.

What all this does tell us is that evolution is not a fact. It is not beyond all shadow of a doubt. But this is what evolutionists claim. And when presented with the science, you can see above how they react.

56 comments:

There are facts of evolution and a theory of evolution. It's very sloppy writing for someone critizing evolution to elide over this important distinction. The evidence from a broad spectrum of disciplines establishes the time line, the radiation, distribution and change and variation in species. Are you denying the simple facts of evolution?

The theory of evolution is an attempt to explain how species change over time. It's the only theory with any explanatory power but it serves well enough for the moment. To challenge the supremacy of the theory of evolution, the effective approach would be to develop an alternative with superior explanatory power.

Dr. Hunter, as well, it seems that proteins, in the course of their non-directed origination, and evolution, from randomly colliding material particles, have somehow learned how to violate the Speed of Light barrier, which then allowed the 'emergence' of Quantum Entanglement/Information from the randomly colliding material particles of the proteins. I'm sure people at the Cern Particle Collider would very much like to know how evolution manage this superluminal feat of having material particles defy the speed of light. It would certainly save them a tremendous amount of money on their energy bill!

Physicists close two loopholes while violating local realism - November 2010Excerpt: The latest test in quantum mechanics provides even stronger support than before for the view that nature violates local realism and is thus in contradiction with a classical worldview.http://www.physorg.com/news/2010-11-physicists-loopholes-violating-local-realism.html

Quantum Measurements: Common Sense Is Not Enough, Physicists Show - July 2009Excerpt: scientists have now proven comprehensively in an experiment for the first time that the experimentally observed phenomena cannot be described by non-contextual models with hidden variables.http://www.sciencedaily.com/releases/2009/07/090722142824.htm

Coherent Intrachain energy migration at room temperature - Elisabetta Collini & Gregory Scholes - University of Toronto - Science, 323, (2009), pp. 369-73Excerpt: The authors conducted an experiment to observe quantum coherence dynamics in relation to energy transfer. The experiment, conducted at room temperature, examined chain conformations, such as those found in the proteins of living cells. Neighbouring molecules along the backbone of a protein chain were seen to have coherent energy transfer. Where this happens quantum decoherence (the underlying tendency to loss of coherence due to interaction with the environment) is able to be resisted, and the evolution of the system remains entangled as a single quantum state.http://www.scimednet.org/quantum-coherence-living-cells-and-protein/

Myosin CoherenceExcerpt: Quantum physics and molecular biology are two disciplines that have evolved relatively independently. However, recently a wealth of evidence has demonstrated the importance of quantum mechanics for biological systems and thus a new field of quantum biology is emerging. Living systems have mastered the making and breaking of chemical bonds, which are quantum mechanical phenomena. Absorbance of frequency specific radiation (e.g. photosynthesis and vision), conversion of chemical energy into mechanical motion (e.g. ATP cleavage) and single electron transfers through biological polymers (e.g. DNA or proteins) are all quantum mechanical effects.http://www.energetic-medicine.net/bioenergetic-articles/articles/63/1/Myosin-Coherence/Page1.html

...it seems that proteins, in the course of their non-directed origination, and evolution, from randomly colliding material particles, have somehow learned how to violate the Speed of Light barrier, which then allowed the 'emergence' of Quantum Entanglement/Information from the randomly colliding material particles of the proteins.

It seems to you may be. What vapid nonsense. "learned to violate the speed of light barrier"!I smell burning straw, Mr. Cunningham!

Well Alan, as for 'vapid nonsense', please do tell, since it is shown that it impossible for material particles to be the 'non-local cause' of quantum entanglement, which non-reductive, non-local, material cause do you postulate to be the 'cause'??? Multiverse, Many-Worlds, m-Theory, String theory??? Please, Don't let the fact of quantum entanglement in proteins upset you too much., I'm sure that you will have no problem ignoring the fact once you can imagine a excuse, any excuse, no matter how far fetched, that let you cling to your atheistic belief!

Yes, Dr Hunter, it is all about the supremacy of world view - do you have to believe that God created the world? If so, then we have to obey the commands of God in the Bible. That is too difficult to accept for some, so they will believe and argue anything, ignore any evidence to avoid submitting to God. That has never been news. Nevertheless, thank you for the unfiltered science the atheists need to suppress..

The evolutionary shortfall is between 27 orders of magnitude and 49 orders of magnitude, according to the evolutionist’s own numbers. So these probabilities do not come from me, they come from evolutionists. In fact, this same evolutionist had once recommended the paper which he now disparages. So what an evolutionist writes is good science. But when repeated by a skeptic, it becomes a frivolous “numbers game.”

That's quite a range there, between 27 and 49 orders of magnitude (22 orders of magnitude). That shows that such calculations are so dependent on the underlying assumptions as to be unreliable.

I did not disparage the paper

How much of protein sequence space has been explored by life on Earth? by Dryden et al..

what I was disparaging was Dr Hunter's entire "improbability of protein evolution" argument.

Here's what I said about the paper originally, in the comment linked above by Dr Hunter:

"Probability calculations such as this depend on the model being proposed. Dr Hunter's calculation is based on the arbitrary assumption that the entirety of protein sequence space must be randomly sampled to yield functional proteins. But the incorporation of some limiting factors into the model yields a different outcome..."

In that paper the authors evaluated a range of assumptions regarding "number of organisms, genome size, mutation rate and the number of functionally distinct classes of amino acids." And, lo and behold, different assumptions yielded widely different probabilities. In a later post, Dr Hunter criticized several of those assumptions, arguing that they were too optimistic. That's fair, but it underscores my point: probability calculations are only as good as the qualifying assumptions behind them.

Apropos of that, there seems to be equivocation in these recent posts between a hypothetical abiotic origin by pure chance of any protein at all (Dr Hunter's favorite example is one composed of 100 amino acids) and the plausibility of the expansion of protein sequences given the availability of mutational and selective resources during the history of life. It was the latter topic that Dryden and coworkers addressed.

Apropos of that, there seems to be equivocation in these recent posts between a hypothetical abiotic origin by pure chance of any protein at all (Dr Hunter's favorite example is one composed of 100 amino acids) and the plausibility of the expansion of protein sequences given the availability of mutational and selective resources during the history of life. It was the latter topic that Dryden and coworkers addressed.

What's even better is that the authors knew that slimy Creationists would deliberately try and misuse their numbers, and warned about it at the end of the paper:

Dryden et al: "Finally, we conclude that the number 20^100 and similar large numbers (e.g. Salisbury 1969; Maynard Smith 1970; Mandecki 1998; Luisi 2003; Carrier 2004; de Duve 2005) are simply ‘straw men’ advanced to initiate discussion in the same spirit as the ‘Levinthal paradox’ of protein folding rates (Levinthal 1969; Zwanzig et al. 1992). 20^100 is now no more useful than the approximate 2×10^1834097 books present in Borges' (1999) fantastical ‘Library of Babel’ and has no connection with the real world of amino acids and proteins. Hence, we hope that our calculation will also rule out any possible use of this big numbers ‘game’ to provide justification for postulating divine intervention. "

Alan, where is it written that a scientific theory can only be challenged if an alternative exists? Doesn't the history of science show that challenges to the dominant theory often lead to better theories? I see this as just an excuse for evolutionists to keep evolution from criticism.

The fact/theory deception is quite the crafty little knot of rhetoric that evolutionists have weaved together. Sure it is a fact that things change, but automatically assuming UCD based on some changing alleles is a leap of faith that is not grounded in the evidence.

You said, "The evidence from a broad spectrum of disciplines establishes the time line, the radiation, distribution and change and variation in species. Are you denying the simple facts of evolution?"

--Wow, that sure sounds impressive, even intimidating! But break it down and it is a big pile of hogwash.

Darwins tree of life is an archaic 19-20th century relic that has been found to be inaccurate from the based to the branches.

Phylogeny based on morphology was a slam dunk for evolutionists, however, genetic testing often yields contradictory findings (the sea squirt is one example, humans another, etc)

The hogwash about not challenging evolution until an alternative is suggested is a form of intimidation and manipulation towards those scientists that wish to speak more openly and critically of the immense problems with evolution.

Alan, where is it written that a scientific theory can only be challenged if an alternative exists? Doesn't the history of science show that challenges to the dominant theory often lead to better theories?

Go on Tedford, give us a list of scientific theories that were successfully challenged without a competing theory ready to take its place. We'll wait.

I see this as just an excuse for evolutionists to keep evolution from criticism

Of course you do, because you're an idiot. Science thrives on and progresses due to informed constructive criticism. But the simple fact is, unsupported blustering rhetoric from a scientifically illiterate pastor that he personally doesn't believe the evidence doesn't qualify.

What difference does it make that he's a Nobel prize winner, since his Nobel (and expertise) is in superconductor physics and has nothing even remotely connected to climatology? You might as well crow that Sam the Lawyer or Fred the Dentist denies global warming.

Another typical Faux News piece of crappola written for the mouth-breathers like you Tedford. Looks like you swallowed it uncritically as usual.

No. Like Darwinism, it is quack science driven by a preconceived agenda.

Ah, The Hidden Agenda. According to the Bible Prophecy Blog:

"...the massive “global warming alarmist” campaign that attempts to impose socialistic globalist control over nations, businesses, and your lifestyle."----"The globalist think tank, the Club of Rome, published in 1993 “The First Global Revolution” that clearly outlined the global elite’s plans to use the invented crisis of “global warming” to stampede humanity toward their hidden goal – global socialist government. The chilling language reveals the cynical propaganda plans of those who seek to impose global socialist government on everyone."

Actually Tedford that's just your head spinning due to the lack of blood flow to your brain that killed most of its cells.

Face it Tedford, you're a scientific illiterate doing nothing but pushing your religious agenda. If your Bible said "man shall not stray from the ground" you'd be hanging out at airports and picketing the pilots, telling them heavier-than-air flight has been falsified and is impossible.

Alan, where is it written that a scientific theory can only be challenged if an alternative exists?

It isn't and I didn't say so either. You are welcome to knock holes in the theory if you can. I said "the effective approach would be to develop an alternative with superior explanatory power." There is a movement, "Intelligent Design", which may become something more than a cover for religious fundamentalist propaganda if it ever tried that approach. I'm not holding my breath.

I am just puzzled why fundamentalists like CH can't just accept reality rather than pretending that the world is as they wish it to be. Their choice.

Alan said, "There is a movement, "Intelligent Design", which may become something more than a cover for religious fundamentalist propaganda if it ever tried that approach."

--

What approach would that be? I'm not sure if you actually understand what the ID theorists say. Do you equate ID theorists with Young Earth Creationists, or what? Would you consider any attempt at making a case for a designer off limits by default?

The story of evolution has very serious issues and evolutionists are in public denial of these. Rather than stick to the science, Darwinists always retreat into the mode of making it into a religion against science debate.

The reality is that evolution would be bad science even if the Bible didn't exist.

CH: As usual divine intervention is the target and ruling it out is the motivation for the pseudo science. For evolution’s theoretical core, as Lakatos would put it, is not gradualism or selection, but naturalism.

Apparently, you cannot see the forest for the trees. Evolution is the explanation for how the knowledge to create different species as found in the genome was *created*.

For example, why are the first organisms we've discovered single cell organisms? Why do we not observe them first appearing at the same time with complex multicellular organisms in the fossil record? Why to the remainder of organisms appear in the order that they do?

Neo-Darwinism explains these observations in that the knowledge of how to build complex multicellular organisms had yet to be created. Specifically, knowledge creation is explained variation and error testing. In the case of Neo-Darwinism, the specific mechanisms include random mutations, HGT, duplications along with natural selection.

We suspect that specific environmental conditions can significantly speed up creation of knowledge, such as a mass extinction event. This still would not falsify the theory of that the knowledge in the genome was created by evolutionary mechanisms. So no, the "core" of evolutionary theory isn't necessarily gradualism. Nor is it necessarily naturalism as that would require assumptions of what nature would not be capable of doing in the distant past of future, based on observations of what we've observed nature having done in the past. This would be subject to the problem of induction.

On the other hand, how does ID explain these same observations? Do ID proponents think the designer knew how to create complex multicellular organisms, but simply decided not to? He could have created organisms in any order he wanted, but intentionally decided on what we observe? Did he know how, but could not? Or do they think the designer ended up created the knowledge as he went along, just as we do in science?

If variations of the former, we can distill this down to variant of "thats just what the designer must have wanted." Nor does the latter seem to be a likely claim, as it wouldn't leave the door open wide enough to accommodate their favorite theological omniscient designer.

Rather, what we get is that "we cannot know how the knowledge found in the genome was created", which is an implicit claim that biological organisms were created in such a way that makes a theory of how the knowledge found in their genome was created is impossible. This represents a supposed boundary where human reasoning and problem solving cannot pass.

it's the equivalent to saying atoms were created in such a way as to make atomic theory impossible or photons were created in such a way that the theory of optics is impossible, etc. it's an arbitrary and disingenuous claim.

Hunter: Evolution, even with extremely optimistic assumptions, is easily the worst scientific theory. One can find theories that may be unlikely, but evolution’s shortfall, of 27 orders of magnitude (and that is assuming a biosphere teeming with life already exists), is extreme.

Even if we take Hunter's numbers game at face value, there are scientific theories with even larger mismatches. Current theoretical estimates of the cosmological constant are off by a factor of 10^{120}. Does that make particle physics or astrophysics a failed science? I don't think so. And in the past, physics faced the ultraviolet catastrophe: the energy density of electromagnetic radiation was off by infinitely many orders of magnitude. Did physics fail? So far as I know, it's alive and well.

At any point in time, science has its leading edge. Creationists love pointing to unsolved problems at the edge. When those problems are eventually solved, they step toward the new position of the edge and point out problems there. It's an endless process. Enjoy your game, Cornelius. I hope you get compensated for spending your time productively.

CH: CH: As usual divine intervention is the target and ruling it out is the motivation for the pseudo science.

Actually, what we're looking for is an explanation as to why God would divinely intervene in one situation, rather than another, and to cause one specific outcome, rather than another.

Why wouldn't God directly intervene every time in the case of the phenomena of gravity? Could it due to the fact that this would result in God directly pulling people to their deaths, crushing people with heavy objects, etc, rather than taking an impartial stance?

What about the case of chemical reactions? Or any other field in science? Why wouldn't God divinely intervene here as well?

It's as if you hold a presupposition that God would NOT intervene in a way that we could mathematically modeled or predict? But why would you hold this assumption in the first place?

Why the insistance that the first proteins were full-sized modern domains, when catalytic peptides, peptides that assemble into larger folds, and even amyloids (had Dr. Hunter not selectively read the article, see quote below) demonstrate this assumption is fundamentally flawed. The big numbers game is really that, when you fabricate the knowledge that first functional proteins must have been of modern size and complexity.

"Eisenberg, Dobson and others have speculated that the self-complementary stickiness of these short segments might have made them useful building blocks in the earliest stages of life on Earth. Moreover, reports have started to emerge of proteins that function normally in the amyloid state, for example some pituitary hormones. “We know by now of over two dozen native amyloids, so this state is clearly used by biology in a functional way as well as a dysfunctional way,” says Eisenberg”

"the effective approach would be to develop an alternative [theory] with superior explanatory power." It's in the comment that you quoted.

I'm not sure if you actually understand what the ID theorists say.

I'll entertain that possibility, along with you and ID "theorists". I understood Paul Nelson quite well when he said:

Easily the biggest challenge facing the ID community is to develop a full-fledged theory of biological design. We don’t have such a theory right now, and that’s a real problem. Without a theory, it’s very hard to know where to direct your research focus. Right now, we’ve got a bag of powerful intuitions, and a handful of notions such as “irreducible complexity” and “specified complexity”—but, as yet, no general theory of biological design.

Scott said, "For example, why are the first organisms we've discovered single cell organisms? Why do we not observe them first appearing at the same time with complex multicellular organisms in the fossil record? Why to the remainder of organisms appear in the order that they do?"

--

Single cell organisms form the foundation for life on earth, so you need them first. They are not an optionally nice thing to have. A strong and vibrate and worldwide population of single cell organisms is a first necessity.

Your mind is in the vortex of the black hole of evolution. If you break out of this mind sucking vortex, you'll see that you have simply interpreted the data to bring you comfort.

Single cell life is complex enough. Let me ask your same question but add a more probing phrase to it....

"why are the first organisms we've discovered single cell organisms, ... and not something less complex?"

Yes, I know... fossils didn't form. Didn't form, or never existed? The results are the same, so that adds zero value to your argument.

Furthermore, the single cell is not of inferior "technology" than what came later. It's not like human designs that tend to get better over time. For example, PC power supplies and batteries have replaced the old and improved over time. Even the Apple company does not have the foresight to develop components that will be used in their devices 25 years from now. Yet the foresight and the complexity of eukaryotes which are utilized in mammals and mankind is astounding.

Life represents the most elegant example of a bottom up hierarchy of modular construction with far, far advanced top down design and foresight.

In human designs we see the Wright brothers airplane .... up to the Space Shuttle. What components of design do they share? Little, and that's a stretch.

Follow my little comparison here... For the evolutionist the prokaryotes and eukaryotes represent the Wright brothers Airplane, man represents the Space Shuttle. But the evidence from the complexity of single cells betray this comparison.

For the creationist, eukaryotes don't represent the Wright brother airplane, but an engine in the space shuttle. There is not this crude to improved view. It's all elegant and useful from the start of life to its most complex creatures. The analogy here is not perfect because the space shuttle engine lacks the elegant modular property of life.

It is a design so advanced that it is not appreciated by some but misinterpreted.

First, just so I'm clear, you're saying that an omnipotent and omniscient being had to make single cell organisms the foundation for life on earth? Is that really you're claiming? How do you know this?

But more importantly, you seem to be implying that an omnipotent and omniscient being that has supposedly always existed had to create single cell organisms *before* creating multicellular organisms? Again, are you really making this claim?

For example if this were true, wouldn't this suggest that God couldn't have created both single cell and multicellular organisms at the exact same time - or had to wait roughly 2.5 billion years to create complex single cell organisms (eukaryotes) *after* first creating simple single cell organisms (prokaryotes), then wait another 1.5 billion years to create multicellular life. Then wait 1 billion years before making complex multicellular animals, then wait another billion years to create hominids (human beings) that look like us today? If either case was necessary, this suggests that God has some limitation which required simpler life to be created *before* more complex life. However, if God wasn't creating the necessary information of how to build these more complex species incrementally, then how do you explain why they were created simpler to more complex or even spread out at all?

Specifically, since God is supposedly omnipotent and omniscient, he would be under no such limitations. Nor would he need nearly 3 billion years to create the knowledge to build multicellular organisms, after single cell organisms, etc. This is because God has supposedly always existed and has always supposedly been omniscient.

Since God has supposedly always exited, then the knowledge of how to create everything from the simplest cells to human beings must have always existed as well. As such, he could have created everything at once since he always supposedly knew how.

For example, he could have created both prokaryotes and eukaryotes at the same time. This is because he would have always had the knowledge of how to build them. Or he could have created Prokaryotes, eukaryotes and multicellular organisms at the same time as he would have always had the knowledge of to build them as well. Or he could have created all forms of life we observe today all at once. Again, this because he supposedly would have always had the knowledge of how to build each and every one of them.

It's important to note that knowledge I'm referring to above couldn't have been created, as this would imply that God was created or that God wasn't always omniscient.

So, my question is, how do you explain why God ended up creating life in the order we actually observe, despite the fact that he always would have had the knowledge to do so all at once, or at intervals of one second, every day, week, month, year, million years, 10 million years, 100 million years, billion years … or an near infinite number of intervals apart?. Why would have God have chosen a timeline that was even remotely close to what we'd expect if evolution really was the explanation for the creation of knowledge in the genome but was actually false, in reality?

How does ID explain this?

Again, Neo-Darwinism explains observations of this particular timeline in that the knowledge of how to create each more complex for of life was created incrementally via RM, duplication, HGT, etc. and natural selection.

Surely, it's not logically impossible that God would create life in exactly this particular timeline, but the question is, why would he do so given that he already had the knowledge? Nor was he limited by resources, already had to many things on his plate, etc. as God is supposedly infinite.

Again, it seems unlikely that you'd claim that the designer had to do it this particular way, otherwise you haven't left the door open wide enough for God.

Neal: "why are the first organisms we've discovered single cell organisms, ... and not something less complex?"

Again, the earliest single celled organisms (Prokaryotes) were less complex than the more complex single celled organisms (eukaryotes ) which appear 2.5 billion years later. For example, unlike eukaryotes, prokaryotes do not have a true nuclei that contains their DNA. In fact the structure of prokaryotes and eukaryotes is so great that it is sometimes considered to be the most important distinction among groups of organisms.

Because we explain the second genetic set of mitochondria DNA found in eukaryote cells with the endosymbiotic association of aerobic bacteria and cyanobacteria within the ancestors of eukaryotes. This is what is referred to as horizontal gene transfer (HGT) of aerobic bacteria.

Neal: Furthermore, the single cell is not of inferior "technology" than what came later. It's not like human designs that tend to get better over time.

Is that so? Then how do you explain the difference between prokaryotic cells and eukaryotic cells as found here?

The prokaryotic cell can be compared to a studio apartment: a one-room living space that has a kitchen area abutting the living room, which converts into a bedroom at night. […]

A eukaryotic cell can be compared to a mansion, where specific rooms are designed for particular activities. The mansion is more diverse in the activities it supports than the studio apartment. It can accommodate overnight guests comfortably and support social activities for adults in the living room or dining room, for children in the playroom. The baby's room is warm and furnished with bright colors and a soft, thick carpet. The kitchen has a stove, a refrigerator and a tile floor. Items are kept in the room that is most appropriate for them, under conditions ideal for the activities in that specific room.

Neal: In human designs we see the Wright brothers airplane .... up to the Space Shuttle. What components of design do they share? Little, and that's a stretch.

Precisely, my point. As human designers, we are free to completely replace all of the parts, while still incorporating previous function. This is because we created the knowledge to reach space after creating the knowledge of how to glide. We can integrate this knowledge, while sharing very little, if anything, which represents the further creation of knowledge.

Note, I'm NOT suggesting that God should have done it some other way that what we observe. Rather I'm asking why he would have done it in a way that was even remotely close to what we would expect if the knowledge of how to build each species was created by evolutionary processes? Again, this would be unnecessary for an omnipotent and omniscient being that has always existed for reasons I outlined above.

Neal: It is a design so advanced that it is not appreciated by some but misinterpreted.

Why must I interpret things I appreciate as having intelligent designers? This simply does not follow.

"Single cell organisms form the foundation for life on earth, so you need them first. They are not an optionally nice thing to have. A strong and vibrate and worldwide population of single cell organisms is a first necessity."

How do you know that? Because science figured it out? You know, the same science that you bash every day? Your imaginary all-powerful god must be really inept if he couldn't just create multi-cellular organisms in the first place.

Your mind is in the vortex of the black hole of religion and denial. If you break out of this mind sucking vortex, you'll see that you have simply interpreted the data to bring you comfort.

The Whole Truth, I'm not bashing science, I'm critical of evolution. Two different things, one science, one fairy tale. Darwinists attempt to make this a science against religion debate to deflect the problems with evolution. This is a pseudo-science vs. science debate.

Do you even realise Theory of Evolution is a theory of BIOLOGY? It has nothing to do with particles and quantum entanglement. You do know this, right...? "====

Unfortunately the TOE is much like a virus which infects whatever it touches. We often here stories using words/terms of Evolution of the planets. Evolution of the Solar System. Evolution of the Universe. Evolution of crystals, whatever.

The bottomline is and always has been Evolution = "No Intelligence Allowed" and that underlying philosophical resentment infects like a deadly plague every science it touches with it's dirty germ infected fingerprints.

Scott, I do appreciate your wording the prokaryotes being less complex than eukaryotes and not using the rather misleading term "simple". However, some people use it in the relative sense, but "less complex" is more precise. Hopefully that was intentional on your part.

Again, the prokaryotes were necessary first before eukaryotes in order to prepare the earth's biosphere and atmosphere for later life forms. Laying the foundation is not evidence for evolution anymore than preparing the foundation of a building is. It's the necessary and wise builder who does so, or the building won't stand for long.

This idea of prokaryotes getting together to form eukaryotes is very problematic. It's not like one person with peanut butter running into another person with a chocolate bar and forming a Reeses peanutbutter cup. What evolutionists miss is that the whole genome of that colony of prokaryotes must change to a reproduce a eukaryote. To simplify greatly, sewing two cats together will not cause the cats to reproduce a two headed cat.

You said, "Rather I'm asking why he would have done it in a way that was even remotely close to what we would expect if the knowledge of how to build each species was created by evolutionary processes?"

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That is because evolutionists have spent much effort cherry picking data that will fit their story and accommodating the story to fit any data that is contradictory. Evolutionists are generous with "free lunches" to some very big problems. Also, Darwin defined a very narrow scope as to how God should have created things. This has created a very powerful illusion (the vortex I spoke of earlier). If a mindset is framed by that illusion, then it appears to make sense. But like a dreaming person, the alarm clock is buzzing and annoying. Rather than make the buzzing (contradictory evidence) part of the dream, the evolutionist needs to wake out of their illusion.

Top down design and bottom up implementation is a closer match to the data.

Neal:Again, the prokaryotes were necessary first before eukaryotes in order to prepare the earth's biosphere and atmosphere for later life forms.

Huh?

Neal, we're talking about an omnipotent and omniscient being. Why was this *necessary*?

If this is the case, wouldn't this mean God couldn't have created the entire universe last Thursday, with the mere appearance of age, implanted memories, etc., and all of it's contents because he had to first prepare the earth's biosphere and atmosphere for later life forms?

Are you really saying this would be impossible for God?

This seems to suggest your approach to biology is parochial rather than universal in scope. From the Wilkipedia entry on Parochialism….

Parochialism means being provincial, being narrow in scope, or considering only small sections of an issue. It may, particularly when used pejoratively, be contrasted to universalism.

In other words, you do not seem to realize the impactions of your own claims, since you apparently haven't really thought them though behind the assumption that they support your position.

Or, as I've said in the past, apparently you do not take your own claims seriously, as any *necessity* to first create prokaryotes to prepare the earth's biosphere for later life forms would represent a *necessary* limitation of God.

Apparently you ether think God has limits or it's unclear what your position really is. So, before we continue, please clarify exactly what you mean by *necessary* in respect to God.

Scott said, "If this is the case, wouldn't this mean God couldn't have created the entire universe last Thursday, with the mere appearance of age, implanted memories, etc., and all of it's contents because he had to first prepare the earth's biosphere and atmosphere for later life forms?"

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I'm certainly not saying that God created the world last Thursday and etc. Where do you get that from?

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You said, "Or, as I've said in the past, apparently you do not take your own claims seriously, as any *necessity* to first create prokaryotes to prepare the earth's biosphere for later life forms would represent a *necessary* limitation of God."

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Why limit God? Could God have instantly created the biosphere? Certainly, but why is he bound to do it that way? Why be stuck in an either/or extreme that dictates either God created everything instantly or he created everything via a process of living organisms. Why not a combination of both?

I believe the evidence shows that he used a varied combination of both. This is illustrated wonderfully throughout the Bible in his workings with mankind. Genesis in the Bible shows a stepwise creation of the biosphere. It has also been my personal experience that God works in many different ways.

The abrupt appearance of prokaryotes early in the fossil record shows just that... an abrupt creative work by God. The abrupt appearance of eukaryotes shows the same thing in the fossil record. It is logical from a design perspective, since eukaryotes depend on prokaryotes in their environment.

If you're stuck in this extreme either/or thinking that would explain a lot of your previous comments. There is nothing Biblical/ theological to say that God couldn't create prokaryotes and then use their God given abilities to prepare the biosphere for eukaryotes. God created a sustainable earth wherein it's organisms provided this sustainability. We know that the prokaryotes had a most definite effect on the biosphere, so what's the big deal with that? It contradicts nothing I've said previously.

Why limit God? Could God have instantly created the biosphere? Certainly, but why is he bound to do it that way? Why be stuck in an either/or extreme that dictates either God created everything instantly or he created everything via a process of living organisms. Why not a combination of both?

That's the beauty of inventing an omniscient, omnipotent god. You can imagine anything you like.

You never really explained what that problem is, but your other arguments suggest that you thought the problem is with the existence of what you think are vanishingly unlikely non-amyloid structures. I am not sure you have read the Dobson and Eisenberg papers carefully since the authors provide an explanation precisely for how the amyloid-causing parts of protein are sequestered in various ways, thus preventing the protein from aggregating. The "amyloid threat" as you call it is simply a reflection of the most thermodynamically stable state of a protein. But as we saw earlier, thermodynamically most stable does not equate to most unlikely and so it's not surprising that proteins avoid this state. The mystery you see here seems to be only perceived and not real.

Pedant, didn't check the previous articles but did you ever respond with what you would consider evidence (even hypothetical, if you must) for a creator? If it did happen, what would you have expected?

If you don't know, then how would you know you haven't already seen it already, but just missed it?

Neal: I'm certainly not saying that God created the world last Thursday and etc. Where do you get that from?

Neal, I didn't say you made that claim. However, you did claim that…

…the prokaryotes were necessary first before eukaryotes in order to prepare the earth's biosphere and atmosphere for later life forms.

…which makes an implicit claim that God couldn't have created the universe last Thursday, with the appearance of age, etc, because he would need to first "prepare the earth's biosphere and atmosphere for later life forms." using eukaryotes. However, if God is omnipotent and omniscient, what would prevent him from doing so?

Neal: Why limit God? Could God have instantly created the biosphere? Certainly, but why is he bound to do it that way?

Huh? You're the one who said something was necessary for God! I'm just pointing it out...

Furthermore, I clearly addressed this when I wrote…

Note, I'm NOT suggesting that God should have done it some other way that what we observe. Rather I'm asking why he would have done it in a way that was even remotely close to what we would expect if the knowledge of how to build each species was created by evolutionary processes? Again, this would be unnecessary for an omnipotent and omniscient being that has always existed for reasons I outlined above.

Again, Neo-Darwinism has and explanation for this. How does ID explain it?

Neal: Why be stuck in an either/or extreme that dictates either God created everything instantly or he created everything via a process of living organisms. Why not a combination of both?

Neal, did you actually read my comment?

Clearly, I'm NOT suck as I wrote…

So, my question is, how do you explain why God ended up creating life in the order we actually observe, despite the fact that he always would have had the knowledge to do so all at once, or at intervals of one second, every day, week, month, year, million years, 10 million years, 100 million years, billion years … or an near infinite number of intervals apart?. Why would have God have chosen a timeline that was even remotely close to what we'd expect if evolution really was the explanation for the creation of knowledge in the genome but was actually false, in reality?

Here I'm clearly pointing out that God could have done it in many ways, and at a near infinite number of intervals, because he always would have had the knowledge to do so.

Instead, it seems that you're the one who's stuck in an extreme regarding the creation of the biosphere vs everything else.

For example, creating "everything instantly" would be creating the entire universe 1 second ago, including implanting false memories that I started writing this comment, not just the biosphere. In other words, God could have created the universe in such a way that some kind of life would have eventually formed, which would also represent some combination of both.

So, again, the question in why this specific combination? Your polarization between the biosphere and everything else appears arbitrary.

Furthermore, what you've just described is essentially the God of the gaps. Knowledge is created in the genome by evolution, unless we actually observe it happening. Then, God must have done it by default.

This would be the equivalent of discovering some highly advanced, transparent calculator and claiming some supernatural being must be lighting up the display *as if* it was doing addition because we did not know exactly how it worked. The underlying principle of addition is the same whether you're doing it in your head, with a pencil and paper, by software running on computer, etc.

So, again, Neo-Darwinism has and explanation for the specific timeline we observe. The knowledge of how to build each species was created in the genome via RM, HGT, gene duplication, etc. and natural selection. How does ID explain it?

Furthermore, what you've just described is essentially the God of the gaps. Knowledge is created in the genome by evolution, unless we [do not] actually observe it happening. Then, God must have done it by default.

Pedant, didn't check the previous articles but did you ever respond with what you would consider evidence (even hypothetical, if you must) for a creator? If it did happen, what would you have expected?

If you don't know, then how would you know you haven't already seen it already, but just missed it?

Thanks for picking up this conversation again. It's kind of fun. As I recall, I did respond to you, but you didn't respond to me, so I thought that you had lost interest.

Yes, if evidence for a creator had appeared before my myopic eyes and I missed it, that evidence might have been there, for sure. However, in my defense, maybe I have been handicapped by a lack of an expectation that I might see any evidence for a creator. I pray that, if such were the case, the creator, being all loving, would have tolerance for my (created, inherited or acquired) fallibility. Do you think that the all-loving and fatherly creator of my fallible self would judge me harshly or show me mercy? If you were the creator, what would you do?

"That’s funny, and perhaps more tongue-in-cheek than serious, but to be clear the amyloid state is caused by the binding of short, self-complementary protein sequences which have a relatively high propensity to stick to themselves. These self-complementary sequences are fairly common. The quaternary binding surfaces to which Behe refers, on the other hand, are far more elusive and difficult to generate at random."

But this doesn't make sense. If binding is difficult to achieve by random modifications of amino acid sequence, it will be equally difficult for binding-to-self as for binding-to-something-else. We just notice the binding-to-self case more often because it can easily lead to fibrils and thus large macromolecular structures and disease.

"Unfortunately the TOE is much like a virus which infects whatever it touches. We often here stories using words/terms of Evolution of the planets. Evolution of the Solar System. Evolution of the Universe. Evolution of crystals, whatever."

The word 'evolution' simply means 'progressive change'. When people talk about 'The evolution of the solar system (for example), they are NOT referring to The Theory of Evolution via Natural Selection, which is a very specific theory and is concerned ONLY with the development of life.

"The bottomline is and always has been Evolution = "No Intelligence Allowed"

All of the attacks on science and evolution by religious people are for one reason and one reason only. Science deals with reality and reality is the last thing that religious people want to face. Their entire belief system is based on fantasies and delusions, and anything that threatens that must be denigrated and eliminated.

And maybe the worst thing is that the people on websites like this one, who constantly attack science, are enjoying and taking advantage of many, many things that science has figured out and made available.

Cornelius G. Hunter is a graduate of the University of Illinois where
he earned a Ph.D. in Biophysics and Computational Biology. He is
Adjunct Professor at Biola University and author of the award-winning Darwin’s God: Evolution and the Problem of Evil. Hunter’s other books include Darwin’s Proof, and his newest book Science’s Blind Spot
(Baker/Brazos Press). Dr. Hunter's interest in the theory of evolution
involves the historical and theological, as well as scientific, aspects
of the theory. His website is http://www.darwins-god.blogspot.com/